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The utility of effective population size in population management 2:estimating demographic history
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. (Höglund lab)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
2016 (English)In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737Article in journal (Refereed) Submitted
Abstract [en]

Elucidating demographic history by tracking the fluctuations of effective population size (Ne) through time has helped uncover interesting insight into the ecology and evolutionary history of a wide array of populations and species. This field of research has seen many exciting methods put forth that together can retrieve the demographic history across many time scales and as such, it is becoming a very useful tool available for conservation practitioners. However, due to the inherent difficulties associated with estimating Ne, the literature can be very technical it is often unclear how methods differ in their assumptions and data requirements. Thus, the choice of which method to use for what purpose can be an extremely difficult one. With this review, we aim to first describe the major methods used to estimate demographic history and clarify their underlying requirements and assumptions. We then highlight some of the overarching motives to understand past Ne fluctuations and we conclude with advice about which methods to use to address these specific motives with a particular focus on the temporal resolution required.

Place, publisher, year, edition, pages
2016.
Keyword [en]
Effective population size, demographic history, population management, Msvar, PSMC, skyline plot
National Category
Ecology
Identifiers
URN: urn:nbn:se:uu:diva-295477OAI: oai:DiVA.org:uu-295477DiVA: diva2:933821
Available from: 2016-06-07 Created: 2016-06-07 Last updated: 2016-08-26Bibliographically approved
In thesis
1. Inferring demographic history and speciation of grouse using whole genome sequences
Open this publication in new window or tab >>Inferring demographic history and speciation of grouse using whole genome sequences
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

From an ecological perspective, knowledge of demographic history is highly valuable because population size fluctuations can be matched to known climatic events, thereby revealing great insight into a species’ reaction to past climate change. This in turn enables us to predict how they might respond to future climate scenarios. Prominently, with the advent of high-throughput sequencing it is now becoming possible to assemble genomes of non-model organisms thereby providing unprecedented resolution to the study of demographic history and speciation. This thesis utilises four species of grouse (Aves, subfamily Tetraoninae) in order to explore the demographic history and speciation within this lineage; the willow grouse, red grouse, rock ptarmigan and the black grouse. I, and my co-authors, begin by reviewing the plethora of methods used to estimate contemporary effective population size (Ne) and demographic history that are available to animal conservation practitioners. We find that their underlying assumptions and necessary input data can bias in their application, and thus we provide a summary of their applicability.

I then use the whole genomes of the black grouse, willow grouse and rock ptarmigan to infer their population dynamics within the last million years. I find three dominant periods that shape their demographic history: early Pleistocene cooling (3-0.9 Mya), the mid-Brunhes event (430 kya) and the last glacial period (110-10 kya). I also find strong signals of local population history – recolonization and subdivision events – affecting their demography. In the subsequent study, I explore the grouse dynamics within the last glacial period in more detail by including more distant samples and using ecological modelling to track habitat distribution changes. I further uncover strong signals of local population history, with multiple fringe populations undergoing severe bottlenecks. I also determine that future climate change is expected to drastically constrict the distribution of the studied grouse.

Lastly, I use whole genome sequencing to uncover 6 highly differentiated regions, containing 7 genes, hinting at their role in adaptation and speciation in three grouse taxa. I also locate a region of low differentiation, containing the Agouti pigmentation gene, indicating its role in the grouse plumage coloration.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. 49 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1391
Keyword
Demographic history, speciation, effective population size, adaptation, willow grouse, red grouse, black grouse, rock ptarmigan, Tetraoninae, conservation genetics, climate change, PSMC, species distribution modelling, FOXP4, Agouti
National Category
Evolutionary Biology Ecology Genetics
Identifiers
urn:nbn:se:uu:diva-299926 (URN)978-91-554-9627-2 (ISBN)
External cooperation:
Public defence
2016-09-16, Lindahlssalen, EBC (Evolutionary Biology Center), Norbyvägen 18B, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2016-08-24 Created: 2016-07-29 Last updated: 2016-08-26

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